Clues such as fossils such as bones, footprints, tar, etc, preserved underground helped inform scientists. You can also count how old a tree is when you cut it open and there are some alive for thousands of years so that is a possible way.
According to Twain man could not have ascended from lower animals (Darwin theory of evolution) because man makes cruel and horrible decisions, rather man descends from Higher animals. He proved his conclusions about man by using specific scientific method, he subjected every postulate itself to the crucial test of actual experiment and have adopted it or rejected it according to the results.